rs11693697

Variant names:

• chr2-102299202-T-C
• rs11693697

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.126 in 152,186 control chromosomes in the GnomAD database, including 1,646 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.13 (1646 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.258

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.126 AC: 19233 AN: 152068 Hom.: 1646 Cov.: 32

Gnomad AFR AF: 0.0338

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.00192

Gnomad SAS AF: 0.0680

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.133

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.126 AC: 19225 AN: 152186 Hom.: 1646 Cov.: 32 AF XY: 0.125 AC XY: 9291 AN XY: 74402

Gnomad4 AFR AF: 0.0337

Gnomad4 AMR AF: 0.115

Gnomad4 ASJ AF: 0.126

Gnomad4 EAS AF: 0.00193

Gnomad4 SAS AF: 0.0674

Gnomad4 FIN AF: 0.200

Gnomad4 NFE AF: 0.187

Gnomad4 OTH AF: 0.132

Alfa AF: 0.163 Hom.: 1104

Bravo AF: 0.117

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.16
DANN	Benign	0.45

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs11693697; hg19: chr2-102915662;